Previous studies have shown that Microbial Electrolysis Cells (MECs) perform better when an anion exchange membrane (AEM) than when a cation exchange membrane (CEM) separates the electrode chambers. Here, we have further studied this phenomenon by comparing two analysis methods for bio-electrochemical systems, based on potential losses and partial system resistances. Our study reconfirmed the large difference in performance between the AEM configuration (2.1 m3 H2 m−3 d−1) and CEM configuration (0.4 m3 H2 m−3 d−1) at 1 V. This better performance was caused mainly by the much lower internal resistance of the AEM configuration (192 mΩ m2) compared to the CEM configuration (435 mΩ m2). This lower internal resistance could be attributed to the lower transport resistance of ions through the AEM compared to the CEM caused by the properties of both membranes. By analyzing the changes in resistances the limitations in an MEC can be identified which can lead to improved cell design and higher hydrogen production rates.